Repast

Recursive Porus Agent Simulation Toolkit

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Here, we provide a list of publications and prjects that have used Repast. If you publish a paper that uses Repast, please let us know, so that we can include it in this list.

• Biotic Population Dynamics and the Theory of Evolution Hector Sabelli, Lazar Kovacevic. Abstract follows.

  We present a theory of evolution and empirical support from empirical studies and computer models of population dynamics. We analyzed published data (Global Population Dynamics Database, NERC Centre for Population Biology) of six animal species and found in five (lynx, muskrat, beaver, salmon, fox) that changes in population size display a pattern characterized by novelty, diversification, non-random complexity, asymmetric statistical distribution, non-uniform recurrence and wavelet plots, and partial autocorrelation. These features characterize bios, as contrasted to random, periodic, chaotic, or random walk patterns. Biotic patterns are also demonstrated in time series generated with multi-agent predator-prey simulations. Biotic patterns have also been found in heartbeat interval series, Schrodinger’s wave function, temporal distribution of galaxies, economic processes, meteorological time series, sequences of bases in DNA, and other data (Sabelli, Bios, A Study of Creation, World Scientific, 2005; see also Thomas et al, this meeting), indicating that they are the expected product of generic natural processes such as those abstracted by lattice action, group opposition, and topological connection. Biotic patterns are generated mathematically with bipolar feedback models such as A(t+1) = sin(A(t)* k * t) (+ A(t) that combine action (recursion), bipolar opposition (trigonometric function) and connection with previous state (+ A(t) term). These observations suggest that population dynamics may be largely determined by bipolar feedback processes. We propose that biological evolution results from the formation and conservation of structure by connections among pre-existing units, and by the generation of novelty and diversity by bipolar (synergistic and antagonistic) feedback interactions --as contrasted to standard evolutionary theory that attributes novelty to random changes and selection to competition and conflict.

  Published paper can be found at here and the source code for the model can be found here

• Patterns in Multiscale Tumor Growth. Chaitanya Athale, Yuri Mansury and Thomas S. Deisboeck have used Repast to consider a multi-scale, multi-cellular model of tumor growth. This work done at the Complex Biosystems Modeling Lab at MIT/MGH Boston (http://biosystems.mit.edu) and has resulted in the following two papers (with more in press) on their work:
  
  1. Athale C, Mansury Y, Deisboeck TS. Simulating the impact of a molecular 'decision-process' on cellular phenotype and multicellular patterns in brain tumors. J Theor Biol. 2005 233(4):469-481. (Abstract).
  2. Athale CA, Deisboeck TS. The effects of EGF-receptor density on multiscale tumor growth patterns. J Theor Biol. 2005. (Abstract).
  The source code and a brief explanation are available here

• Conceptualization and implementation of a multi-agent model to simulate whale-watching activities in the St. Lawrence estuary in Quebec. Anwar, S. M., Jeanneret, C., Parrott, L., and Marceau, D., 2007. Environmental Modeling and Software (accepted for publication).

  Abstract: The Saguenay St. Lawrence Marine Park (SSLMP) and the adjacent Marine Protected Area (MPA) in the St. Lawrence estuary, in Quebec, cover a territory of exceptional biodiversity including 12 species of marine mammals, nearly half of which are considered to be endangered species. Whale-watching trips and other human activities related to commercial shipping, tourism and recreation generate very intensive traffic in the area, which poses cumulative threats to the marine wildlife. This study has been undertaken in collaboration with the Marine Park and the MPA managers to develop a multi-agent system (MAS) to investigate the interactions between the traffic and the marine mammals in the estuary. This paper describes the first prototype version of the proposed MAS model where the focus is on the whale-watching boats. It discusses the conceptual model with its principal components: the physical environment and the boat agents and whale entities, and the implementation of the model with the behavior rules of the agents. In this version of the MAS, the whale-watching boats are represented as cognitive agents while the whales are simple reactive entities. The prototype model was implemented in the agent-based modeling platform RePast. An index, the happiness factor (i.e., the ratio of whale observation time over the trip duration) was designed to measure how successful the boat agents are in achieving their goal. Simulations were run to assess different decision strategies of the boat agents and their impacts on the whales. Results show that cooperative behavior that involves a combination of innovator and imitator strategies yields a higher average happiness factor over non-cooperative, purely innovators, behavior. However, this cooperative behavior creates increased risk for the whale populations in the estuary.

• Social norms, cognitive dissonance and broadcasting: how to influence economic agents. Bertie, A. J., Himmelweit, S. F. and Trigg, A. B. (2006) In Advances in Artifical Economics: The Economy as a Complex Dynamic System (C. Bruun ed). Springer.

  Repast is used to simulate the effects of social influence, cognitive dissonance and broadcasting on the attitudes and behaviour of mothers of pre-school children. The agent-based model is based on Axelrod’s 1997 model of the dissemination of culture.

• Agent Cell. AgentCell is an agent-based Repast model that is useful for studying the relationship between stochastic intracellular processes and the behavior of individual cells. AgentCell is an open source project licensed under the GPL. AgentCell's design and some initial results are discussed in the following journal article:
  Emonet, T., C.M. Macal, M.J. North, C.E. Wickersham, and P. Cluzel, 'AgentCell: A Digital Single-Cell Assay for Bacterial Chemotaxis,' Bioinformatics, Vol. 21, No. 11, pp. 2714-2721, Oxford University Press, Oxford, UK ( March 17, 2005). For more information and downloads please visit http://www.agentcell.org/.
• Appearances Can Be Deceiving: Lessons Learned Re-Implementing Axelrod's 'Evolutionary Approach to Norms.' J.M. Galán and L.R. Izquierdo have published a paper in JASSS based on a model entitled RAEAN (Re-implementation of Axelrod's "Evolutionary Approach to Norms"). This model is designed to replicate and extend Prof. Axelrod’s model using Repast. The paper is avalable on the JASSS website at http://jasss.soc.surrey.ac.uk/8/3/2.html. More information can be found at the previous JASSS link or at http://www.insisoc.org/metanorms/, including a user guide, an API, an applet, and a link to the paper describing their work.
• “Experiences Creating Three Implementations of the Repast Agent Modeling Toolkit,” North, M.J., N.T. Collier, and J.R. Vos. ACM Transactions on Modeling and Computer Simulation, Vol. 16, Issue 1, pp. 1-25, ACM, New York, New York, USA (January 2006).

  Many agent-based modeling and simulation researchers and practitioners have called for varying levels of simulation interoperability ranging from shared software architectures to common agent communications languages. These calls have been at least partially answered by several speci- fications and technologies. In fact, Tanenbaum has remarked that the “nice thing about standards is that there are so many to choose from.” Tanenbaum goes on to say that “if you do not like any of them, you can just wait for next year’s model.” This article does not seek to introduce next year’s model. Rather, the goal is to contribute to the larger simulation community the authors’ accumulated experiences from developing several implementations of an agent-based simulation toolkit. As such, this article focuses on the implementation of simulation architectures rather than agent communications languages. It is hoped that ongoing architecture standards efforts will benefit from this new knowledge and use it to produce architecture standards with increased robustness.

• jECHO. A new version of Holland's ECHO model. jECHO uses the Repast multi-agent framework as the foundation. The site also conatins a copy of the Masters dissertation which describes the analysis, design and implmenetation of jECHO plus some experimentation. jECHO can be found at http://www.brianmcindoe.com.
• Repast in Business Strategy. A simulation of competitive management/business strategy using Repast has been published in Robertson, D. A. (2003) 'Agent-Based Models of a Banking Network as an Example of a Turbulent Environment: The Deliberate vs. Emergent Strategy Debate Revisited', Emergence, 5(2), 56-71. The article can be found at http://www.duncanrobertson.com/research/Emergence.pdf
• Institutional Regime Change. Scott Abernathy (University of Minnesota) and Christopher J. Mackie (Princeton University) are using Repast to study the dynamics of institutional regime changes: how actors and institutions behave when the rules of engagement are changing even as decisions must be made. Their current focus is on the introduction of school-voucher programs into public school jurisdictions. Their latest published work, and a copy of their Repast source code, can be found here.
• Consumer Choice. Professor Robert Axelrod of the University of Michigan used Repast to implement an agent-based model of consumer choice. The question the model explores is "under what conditions can consumers hold producers responsible for producing high quality product, and can intermediaries help the consumers by aggregating information about producers?"
  Contact: Professor Robert Axelrod
  Research Assistant and Programmer: Ross Hammond
• Decision Making in Cloased Political Regimes. Ravi Bhavnani (Political Science, University of Illinois at Urbana Champaign), together with David Backer (Political Science, University of Michigan) and Rick Riolo (Complex Systems, University of Michigan) are using Repast to study the dynamics of decision-making in closed political regimes such as Iraq, North Korea and Syria in a project sponsored by the Department of Defense. Contact Information:
  Ravi Bhavnani, rvib@uiuc.edu
  David Backer, dabacker@umich.edu
  Rick Riolo, rlriolo@umich.edu
• Echo-Like World. Raoul Jean Pierre Bonnal uses Repast for two projects. The first is an implementation of an Echo-like world. The second is the simulation of a pursuit system: a grid of cells over which an object travels such that the system predicts the direction and light on the object in relation to its speed. The system also checks itself for malfunctions and finds a solution for them.
• Stephen Deschamps. Stephan Deschamps from Victoria University Wellington in New Zealand, is using Repast to simulate a knowledge network involving heterogeneous agents such as Small and Medium Enterprises, Universities and Public Research Institutes. The object of the simulation is to study how co-operative research strategies can be implemented among agents with different objectives and rewards, how this affects the dynamics of R&D and innovation, how agents evolve and converge, and what the impact at the system level is. The research will provide a modelisation of the Triple Helix framework, developed by Leydesdorff and Etzkowitz.
• Owen Densmore. Owen Densmore of Sun Microsystems has started using Repast to model self organizing networks, within the context of the Local Knowledge Networking project. His interest in Repast is to bring a new set of tools to analysing parts of computing and networking; especially "self organizing" or "critical" features. He recently did a power-law exploration which came from initial Repast work with a model dynamic network. See backspaces.net for more information about his work.
• Decision Making in Closed Political Regimes. Ravi Bhavnani (Political Science, University of Illinois at Urbana Champaign), together with David Backer (Political Science, University of Michigan) and Rick Riolo (Complex Systems, University of Michigan) are using RePast to study the dynamics of decision-making in closed political regimes such as Iraq, North Korea and Syria in a project sponsored by the Department of Defense. Contact Information: Ravi Bhavnani, rvib@uiuc.edu David Backer, dabacker@umich.edu Rick Riolo, rlriolo@umich.edu
• Lars-Erik Cederman. Lars-Erik Cederman of Harvard University is using Repast to study world politics as a complex system. Specifically, he has modeled state formation, nationalism and the democratic peace with various agent-based models. He taught a course on ABM using Repast at Harvard in 2001-2002.
• The Santa Fe Artificial Stock Market Re-Examined - Suggested Corrections. Norman Ehrentreich of Martin Luther University Halle-Wittenberg. The Santa Fe Artificial Stock Market Re-Examined - Suggested Corrections